#**Community diversity and composition at the haplotype, 3% and 5% lineages for each of the eight taxonomic orders studied**
#####This script gets all scripts of diversity using 8 arthropods order at multi-hierarchical levels
#####We used 8 groups: Arachnda, Coleoptera, Collembola, Diptera, Hemiptera, Hymenoptera, Lepidoptera, and Myriapoda.
library(stats)
library(base)
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(tidyr)
library(knitr)
library(PMCMR)
## PMCMR is superseded by PMCMRplus and will be no longer maintained. You may wish to install PMCMRplus instead.
library(rcdd)
## If you want correct answers, use rational arithmetic.
## See the Warnings sections added to help pages for
## functions that do computational geometry.
library(vegan)
## Loading required package: permute
## Loading required package: lattice
## This is vegan 2.5-2
library(betapart)
library(stringr)
library(permute)
library(lattice)
#**We get the diversity analysis at haplotypes, 3% and 5% lineages in Diptera**
##Source to scripts Diptera and data
source("Diptera/Com_matrixes_data_exploration_Diptera_h_Site.R")
## Warning in Ops.factor(left, right): '>' not meaningful for factors
## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site_h$sample_richness_Site_h, : Ties are present, p-values are
## not corrected.
## Run 0 stress 0.1705049
## Run 1 stress 0.1742834
## Run 2 stress 0.1706164
## ... Procrustes: rmse 0.01675971 max resid 0.05041612
## Run 3 stress 0.1728207
## Run 4 stress 0.1700089
## ... New best solution
## ... Procrustes: rmse 0.07444097 max resid 0.1745926
## Run 5 stress 0.17832
## Run 6 stress 0.1776025
## Run 7 stress 0.1713384
## Run 8 stress 0.1762392
## Run 9 stress 0.1746584
## Run 10 stress 0.1702322
## ... Procrustes: rmse 0.05115378 max resid 0.2231485
## Run 11 stress 0.173807
## Run 12 stress 0.1757302
## Run 13 stress 0.1769855
## Run 14 stress 0.1739728
## Run 15 stress 0.1746207
## Run 16 stress 0.1767848
## Run 17 stress 0.1786834
## Run 18 stress 0.1742968
## Run 19 stress 0.1758702
## Run 20 stress 0.1786646
## *** No convergence -- monoMDS stopping criteria:
## 20: stress ratio > sratmax
## species scores not available
## species scores not available
## species scores not available
## species scores not available
source("Diptera/Com_matrixes_data_exploration_Diptera_3P_Site.R")
## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.03$sample_richness_Site0.03, : Ties are present, p-values
## are not corrected.
## Run 0 stress 0.212727
## Run 1 stress 0.212727
## ... Procrustes: rmse 0.0003655504 max resid 0.001477588
## ... Similar to previous best
## Run 2 stress 0.2518546
## Run 3 stress 0.2447956
## Run 4 stress 0.2245212
## Run 5 stress 0.2129618
## ... Procrustes: rmse 0.006896282 max resid 0.03316547
## Run 6 stress 0.232636
## Run 7 stress 0.2379787
## Run 8 stress 0.2188259
## Run 9 stress 0.2127269
## ... New best solution
## ... Procrustes: rmse 8.417947e-05 max resid 0.0003002356
## ... Similar to previous best
## Run 10 stress 0.2197332
## Run 11 stress 0.2199862
## Run 12 stress 0.2389229
## Run 13 stress 0.2225666
## Run 14 stress 0.2127269
## ... Procrustes: rmse 0.0002897773 max resid 0.001438204
## ... Similar to previous best
## Run 15 stress 0.2245212
## Run 16 stress 0.2129648
## ... Procrustes: rmse 0.007687908 max resid 0.03785052
## Run 17 stress 0.2502881
## Run 18 stress 0.2199861
## Run 19 stress 0.2127269
## ... New best solution
## ... Procrustes: rmse 0.0001687952 max resid 0.0007165534
## ... Similar to previous best
## Run 20 stress 0.2127272
## ... Procrustes: rmse 0.0001697598 max resid 0.0006759932
## ... Similar to previous best
## *** Solution reached
## species scores not available
## species scores not available
## species scores not available
## species scores not available
source("Diptera/Com_matrixes_data_exploration_Diptera_5P_Site.R")
## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.05$sample_richness_Site0.05, : Ties are present, p-values
## are not corrected.
## Run 0 stress 0.2150555
## Run 1 stress 0.2150556
## ... Procrustes: rmse 0.0001500731 max resid 0.0004548274
## ... Similar to previous best
## Run 2 stress 0.2150555
## ... Procrustes: rmse 8.383381e-05 max resid 0.0002804627
## ... Similar to previous best
## Run 3 stress 0.2270005
## Run 4 stress 0.2351285
## Run 5 stress 0.2296127
## Run 6 stress 0.2150555
## ... Procrustes: rmse 6.604374e-05 max resid 0.0003030265
## ... Similar to previous best
## Run 7 stress 0.2150555
## ... Procrustes: rmse 4.966338e-05 max resid 0.000167786
## ... Similar to previous best
## Run 8 stress 0.216303
## Run 9 stress 0.2580705
## Run 10 stress 0.2188767
## Run 11 stress 0.2171952
## Run 12 stress 0.2282902
## Run 13 stress 0.2176331
## Run 14 stress 0.2158436
## Run 15 stress 0.2187359
## Run 16 stress 0.2316618
## Run 17 stress 0.2158436
## Run 18 stress 0.2338777
## Run 19 stress 0.2255358
## Run 20 stress 0.2260855
## *** Solution reached
## species scores not available
## species scores not available
## species scores not available
## species scores not available
#**We get the diversity analysis at haplotypes, 3% and 5% lineages in Collembola**
##Source to scripts Collembola and data
source("Collembola/Com_matrixes_data_exploration_Collembola_h_Site.R")
## Warning in Ops.factor(left, right): '>' not meaningful for factors
## Warning in Ops.factor(left, right): Expected 4 pieces. Additional pieces
## discarded in 42 rows [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
## 16, 17, 18, 19, 20, ...].
## Warning in Ops.factor(left, right): Expected 4 pieces. Additional pieces
## discarded in 42 rows [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
## 16, 17, 18, 19, 20, ...].
## Warning in Ops.factor(left, right): Expected 4 pieces. Additional pieces
## discarded in 42 rows [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
## 16, 17, 18, 19, 20, ...].
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site_h_Collembola$sample_richness_Site_h, : Ties are present, p-
## values are not corrected.
## Run 0 stress 0.1042231
## Run 1 stress 0.1043325
## ... Procrustes: rmse 0.009088366 max resid 0.04961481
## Run 2 stress 0.1043118
## ... Procrustes: rmse 0.08305627 max resid 0.199973
## Run 3 stress 0.1043253
## ... Procrustes: rmse 0.008185306 max resid 0.04418749
## Run 4 stress 0.1042262
## ... Procrustes: rmse 0.00099368 max resid 0.005778975
## ... Similar to previous best
## Run 5 stress 0.1043347
## ... Procrustes: rmse 0.009319234 max resid 0.05099372
## Run 6 stress 0.104336
## ... Procrustes: rmse 0.08279228 max resid 0.2000422
## Run 7 stress 0.1043367
## ... Procrustes: rmse 0.08274708 max resid 0.2000752
## Run 8 stress 0.1204174
## Run 9 stress 0.1043097
## ... Procrustes: rmse 0.08299686 max resid 0.2000107
## Run 10 stress 0.1043095
## ... Procrustes: rmse 0.08294348 max resid 0.200047
## Run 11 stress 0.1043085
## ... Procrustes: rmse 0.08288335 max resid 0.200116
## Run 12 stress 0.1043326
## ... Procrustes: rmse 0.009098066 max resid 0.04967263
## Run 13 stress 0.1221812
## Run 14 stress 0.10432
## ... Procrustes: rmse 0.00732658 max resid 0.03897726
## Run 15 stress 0.1043227
## ... Procrustes: rmse 0.007779144 max resid 0.04173142
## Run 16 stress 0.1042254
## ... Procrustes: rmse 0.0008635217 max resid 0.005017736
## ... Similar to previous best
## Run 17 stress 0.1181587
## Run 18 stress 0.1043348
## ... Procrustes: rmse 0.009253986 max resid 0.05059962
## Run 19 stress 0.1043097
## ... Procrustes: rmse 0.08299373 max resid 0.2000132
## Run 20 stress 0.1216131
## *** Solution reached
## species scores not available
## species scores not available
## species scores not available
## species scores not available
source("Collembola/Com_matrixes_data_exploration_Collembola_3P_Site.R")
## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.03_Collembola$sample_richness_Site0.03, : Ties are present,
## p-values are not corrected.
## Run 0 stress 0.1037297
## Run 1 stress 0.10641
## Run 2 stress 0.109493
## Run 3 stress 0.10641
## Run 4 stress 0.1096296
## Run 5 stress 0.1105657
## Run 6 stress 0.1065262
## Run 7 stress 0.108074
## Run 8 stress 0.1089304
## Run 9 stress 0.110051
## Run 10 stress 0.1064129
## Run 11 stress 0.1163356
## Run 12 stress 0.1094158
## Run 13 stress 0.1040404
## ... Procrustes: rmse 0.01599745 max resid 0.09587982
## Run 14 stress 0.1103509
## Run 15 stress 0.1069449
## Run 16 stress 0.1175932
## Run 17 stress 0.1094139
## Run 18 stress 0.1096315
## Run 19 stress 0.1096867
## Run 20 stress 0.103736
## ... Procrustes: rmse 0.001806573 max resid 0.009240665
## ... Similar to previous best
## *** Solution reached
## species scores not available
## species scores not available
## species scores not available
## species scores not available
source("Collembola/Com_matrixes_data_exploration_Collembola_5P_Site.R")
## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.05_Collembola$sample_richness_Site0.05, : Ties are present,
## p-values are not corrected.
## Run 0 stress 0.1206288
## Run 1 stress 0.1207496
## ... Procrustes: rmse 0.06438135 max resid 0.212615
## Run 2 stress 0.1247856
## Run 3 stress 0.1281347
## Run 4 stress 0.1242398
## Run 5 stress 0.1249398
## Run 6 stress 0.1244363
## Run 7 stress 0.1235641
## Run 8 stress 0.1300619
## Run 9 stress 0.1207964
## ... Procrustes: rmse 0.03218294 max resid 0.1662396
## Run 10 stress 0.1255732
## Run 11 stress 0.1206513
## ... Procrustes: rmse 0.002323895 max resid 0.01086069
## Run 12 stress 0.1273057
## Run 13 stress 0.1209382
## ... Procrustes: rmse 0.02715845 max resid 0.1659724
## Run 14 stress 0.1243932
## Run 15 stress 0.1205558
## ... New best solution
## ... Procrustes: rmse 0.01577207 max resid 0.09109231
## Run 16 stress 0.1257516
## Run 17 stress 0.1207963
## ... Procrustes: rmse 0.02818576 max resid 0.1680564
## Run 18 stress 0.1228196
## Run 19 stress 0.1244352
## Run 20 stress 0.1249346
## *** No convergence -- monoMDS stopping criteria:
## 20: stress ratio > sratmax
## species scores not available
## species scores not available
## species scores not available
## species scores not available
#**We get the diversity analysis at haplotypes, 3% and 5% lineages in Arachnida**
##Source to scripts Arachnida and data
source("Arachnida/Com_matrixes_data_exploration_Arachnida_h_Site.R")
## Warning in Ops.factor(left, right): '>' not meaningful for factors
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site_h_Arachnida$sample_richness_Site_h, : Ties are present, p-
## values are not corrected.
## Run 0 stress 0.1640223
## Run 1 stress 0.1828367
## Run 2 stress 0.1660367
## Run 3 stress 0.1811127
## Run 4 stress 0.1699014
## Run 5 stress 0.1679739
## Run 6 stress 0.1868526
## Run 7 stress 0.1648388
## Run 8 stress 0.1669304
## Run 9 stress 0.1679123
## Run 10 stress 0.1763698
## Run 11 stress 0.1668807
## Run 12 stress 0.166208
## Run 13 stress 0.1674261
## Run 14 stress 0.1800728
## Run 15 stress 0.1758463
## Run 16 stress 0.1674258
## Run 17 stress 0.1809075
## Run 18 stress 0.1705784
## Run 19 stress 0.1738086
## Run 20 stress 0.1762148
## *** No convergence -- monoMDS stopping criteria:
## 20: stress ratio > sratmax
## species scores not available
## species scores not available
## species scores not available
## species scores not available
source("Arachnida/Com_matrixes_data_exploration_Arachnida_3P_Site.R")
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.03_Arachnida$sample_richness_Site0.03, : Ties are present,
## p-values are not corrected.
## Run 0 stress 0.1922801
## Run 1 stress 0.2020944
## Run 2 stress 0.2005619
## Run 3 stress 0.192182
## ... New best solution
## ... Procrustes: rmse 0.01608043 max resid 0.06963253
## Run 4 stress 0.1922696
## ... Procrustes: rmse 0.008850614 max resid 0.04081894
## Run 5 stress 0.1937838
## Run 6 stress 0.1923497
## ... Procrustes: rmse 0.01115861 max resid 0.0428627
## Run 7 stress 0.2105356
## Run 8 stress 0.1922794
## ... Procrustes: rmse 0.01607519 max resid 0.06957806
## Run 9 stress 0.1922817
## ... Procrustes: rmse 0.01606974 max resid 0.0696413
## Run 10 stress 0.1961158
## Run 11 stress 0.1965957
## Run 12 stress 0.1937838
## Run 13 stress 0.196594
## Run 14 stress 0.200564
## Run 15 stress 0.1967166
## Run 16 stress 0.1986574
## Run 17 stress 0.1922698
## ... Procrustes: rmse 0.008684918 max resid 0.0403805
## Run 18 stress 0.1966405
## Run 19 stress 0.1923329
## ... Procrustes: rmse 0.01733909 max resid 0.06970682
## Run 20 stress 0.2038669
## *** No convergence -- monoMDS stopping criteria:
## 20: stress ratio > sratmax
## species scores not available
## species scores not available
## species scores not available
## species scores not available
source("Arachnida/Com_matrixes_data_exploration_Arachnida_5P_Site.R")
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.05_Arachnida$sample_richness_Site0.05, : Ties are present,
## p-values are not corrected.
## Run 0 stress 0.199876
## Run 1 stress 0.2087461
## Run 2 stress 0.1998755
## ... New best solution
## ... Procrustes: rmse 0.000164834 max resid 0.0008777296
## ... Similar to previous best
## Run 3 stress 0.205641
## Run 4 stress 0.2098513
## Run 5 stress 0.1998764
## ... Procrustes: rmse 0.0003774437 max resid 0.002133885
## ... Similar to previous best
## Run 6 stress 0.2024718
## Run 7 stress 0.2184258
## Run 8 stress 0.2141527
## Run 9 stress 0.1992423
## ... New best solution
## ... Procrustes: rmse 0.02204456 max resid 0.08480384
## Run 10 stress 0.2255285
## Run 11 stress 0.1992462
## ... Procrustes: rmse 0.003695492 max resid 0.01736026
## Run 12 stress 0.213992
## Run 13 stress 0.1998778
## Run 14 stress 0.2081459
## Run 15 stress 0.2103101
## Run 16 stress 0.2256752
## Run 17 stress 0.1998777
## Run 18 stress 0.224641
## Run 19 stress 0.211866
## Run 20 stress 0.1992425
## ... Procrustes: rmse 8.562322e-05 max resid 0.0002876852
## ... Similar to previous best
## *** Solution reached
## species scores not available
## species scores not available
## species scores not available
## species scores not available
#**We get the diversity analysis at haplotypes, C3% and 5% lineages in Hemiptera**
##Source to scripts Hemiptera and data
source("Hemiptera/Com_matrixes_data_exploration_Hemiptera_h_Site.R")
## Warning in Ops.factor(left, right): '>' not meaningful for factors
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site_h$sample_richness_Site_h, : Ties are present, p-values are
## not corrected.
## Run 0 stress 0.1232448
## Run 1 stress 0.1302921
## Run 2 stress 0.120326
## ... New best solution
## ... Procrustes: rmse 0.05008299 max resid 0.1301977
## Run 3 stress 0.1338129
## Run 4 stress 0.1231923
## Run 5 stress 0.1206297
## ... Procrustes: rmse 0.0302274 max resid 0.08773975
## Run 6 stress 0.1201466
## ... New best solution
## ... Procrustes: rmse 0.02241538 max resid 0.08305554
## Run 7 stress 0.1323811
## Run 8 stress 0.1300975
## Run 9 stress 0.1251024
## Run 10 stress 0.1224937
## Run 11 stress 0.1282869
## Run 12 stress 0.1239621
## Run 13 stress 0.1217274
## Run 14 stress 0.1205673
## ... Procrustes: rmse 0.04039636 max resid 0.1197719
## Run 15 stress 0.1218062
## Run 16 stress 0.1203239
## ... Procrustes: rmse 0.02203384 max resid 0.08123151
## Run 17 stress 0.1288358
## Run 18 stress 0.1211859
## Run 19 stress 0.1267372
## Run 20 stress 0.1226463
## *** No convergence -- monoMDS stopping criteria:
## 20: stress ratio > sratmax
## species scores not available
## species scores not available
## species scores not available
## species scores not available
## species scores not available
source("Hemiptera/Com_matrixes_data_exploration_Hemiptera_3P_Site.R")
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.03$sample_richness_Site0.03, : Ties are present, p-values
## are not corrected.
## Run 0 stress 0.1638168
## Run 1 stress 0.1690172
## Run 2 stress 0.1674213
## Run 3 stress 0.1662174
## Run 4 stress 0.1679385
## Run 5 stress 0.1726117
## Run 6 stress 0.1679825
## Run 7 stress 0.1727626
## Run 8 stress 0.1664749
## Run 9 stress 0.1665281
## Run 10 stress 0.1661126
## Run 11 stress 0.1657984
## Run 12 stress 0.1717067
## Run 13 stress 0.1672803
## Run 14 stress 0.1698128
## Run 15 stress 0.1658208
## Run 16 stress 0.1712985
## Run 17 stress 0.1707134
## Run 18 stress 0.1671109
## Run 19 stress 0.1677347
## Run 20 stress 0.1688403
## *** No convergence -- monoMDS stopping criteria:
## 20: stress ratio > sratmax
## species scores not available
## species scores not available
## species scores not available
## species scores not available
## species scores not available
source("Hemiptera/Com_matrixes_data_exploration_Hemiptera_5P_Site.R")
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.05$sample_richness_Site0.05, : Ties are present, p-values
## are not corrected.
## Run 0 stress 0.1748273
## Run 1 stress 0.1809059
## Run 2 stress 0.1766329
## Run 3 stress 0.1761215
## Run 4 stress 0.1765299
## Run 5 stress 0.1737685
## ... New best solution
## ... Procrustes: rmse 0.06345736 max resid 0.1911859
## Run 6 stress 0.176096
## Run 7 stress 0.1809846
## Run 8 stress 0.1752628
## Run 9 stress 0.1750244
## Run 10 stress 0.1844015
## Run 11 stress 0.1743885
## Run 12 stress 0.1752702
## Run 13 stress 0.1819352
## Run 14 stress 0.1789328
## Run 15 stress 0.1754737
## Run 16 stress 0.1775709
## Run 17 stress 0.1828539
## Run 18 stress 0.1744865
## Run 19 stress 0.1764935
## Run 20 stress 0.1766478
## *** No convergence -- monoMDS stopping criteria:
## 2: no. of iterations >= maxit
## 18: stress ratio > sratmax
## species scores not available
## species scores not available
## species scores not available
## species scores not available
## species scores not available
#**We get the diversity analysis at haplotypes, 3% and 5% lineages in Hymenoptera**
##Source to scripts Hymenoptera and data
source("Hymenoptera/Com_matrixes_data_exploration_Hymenoptera_h_Site.R")
## Warning in Ops.factor(left, right): '>' not meaningful for factors
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site_h$sample_richness_Site_h, : Ties are present, p-values are
## not corrected.
## Run 0 stress 9.544494e-05
## Run 1 stress 9.124703e-05
## ... New best solution
## ... Procrustes: rmse 0.0001032763 max resid 0.000222908
## ... Similar to previous best
## Run 2 stress 9.58561e-05
## ... Procrustes: rmse 6.953301e-05 max resid 0.0001774538
## ... Similar to previous best
## Run 3 stress 9.90905e-05
## ... Procrustes: rmse 8.437803e-05 max resid 0.0002251801
## ... Similar to previous best
## Run 4 stress 9.593851e-05
## ... Procrustes: rmse 7.433648e-05 max resid 0.0001542497
## ... Similar to previous best
## Run 5 stress 7.873589e-05
## ... New best solution
## ... Procrustes: rmse 9.706036e-05 max resid 0.000362411
## ... Similar to previous best
## Run 6 stress 9.125645e-05
## ... Procrustes: rmse 8.764146e-05 max resid 0.0002089603
## ... Similar to previous best
## Run 7 stress 9.342967e-05
## ... Procrustes: rmse 6.787735e-05 max resid 0.0001986684
## ... Similar to previous best
## Run 8 stress 7.610741e-05
## ... New best solution
## ... Procrustes: rmse 7.204226e-05 max resid 0.000337471
## ... Similar to previous best
## Run 9 stress 8.648399e-05
## ... Procrustes: rmse 7.135763e-05 max resid 0.0002847584
## ... Similar to previous best
## Run 10 stress 8.962412e-05
## ... Procrustes: rmse 7.045388e-05 max resid 0.0002541278
## ... Similar to previous best
## Run 11 stress 9.905539e-05
## ... Procrustes: rmse 7.877037e-05 max resid 0.0001868187
## ... Similar to previous best
## Run 12 stress 8.928782e-05
## ... Procrustes: rmse 8.783306e-05 max resid 0.0003403028
## ... Similar to previous best
## Run 13 stress 9.109839e-05
## ... Procrustes: rmse 8.596034e-05 max resid 0.0002847826
## ... Similar to previous best
## Run 14 stress 9.233857e-05
## ... Procrustes: rmse 7.720616e-05 max resid 0.0001478097
## ... Similar to previous best
## Run 15 stress 9.986097e-05
## ... Procrustes: rmse 7.797687e-05 max resid 0.0001909345
## ... Similar to previous best
## Run 16 stress 8.946285e-05
## ... Procrustes: rmse 7.865021e-05 max resid 0.0001611864
## ... Similar to previous best
## Run 17 stress 9.13265e-05
## ... Procrustes: rmse 7.104941e-05 max resid 0.0001676933
## ... Similar to previous best
## Run 18 stress 9.553627e-05
## ... Procrustes: rmse 8.913428e-05 max resid 0.0003027862
## ... Similar to previous best
## Run 19 stress 9.43658e-05
## ... Procrustes: rmse 7.132551e-05 max resid 0.0001743736
## ... Similar to previous best
## Run 20 stress 9.743884e-05
## ... Procrustes: rmse 5.242867e-05 max resid 0.0001410682
## ... Similar to previous best
## *** Solution reached
## Warning in metaMDS(beta.pair$beta.sim): stress is (nearly) zero: you may
## have insufficient data
## species scores not available
## species scores not available
## Run 0 stress 0.1734477
## Run 1 stress 0.1852592
## Run 2 stress 0.1717926
## ... New best solution
## ... Procrustes: rmse 0.08052484 max resid 0.2659881
## Run 3 stress 0.1801441
## Run 4 stress 0.1842457
## Run 5 stress 0.1757073
## Run 6 stress 0.177248
## Run 7 stress 0.1760273
## Run 8 stress 0.1818146
## Run 9 stress 0.1773927
## Run 10 stress 0.1725281
## Run 11 stress 0.1789951
## Run 12 stress 0.1775665
## Run 13 stress 0.1723463
## Run 14 stress 0.1757022
## Run 15 stress 0.1788915
## Run 16 stress 0.1753499
## Run 17 stress 0.1707388
## ... New best solution
## ... Procrustes: rmse 0.03237597 max resid 0.1090247
## Run 18 stress 0.1855473
## Run 19 stress 0.1747117
## Run 20 stress 0.186251
## *** No convergence -- monoMDS stopping criteria:
## 1: no. of iterations >= maxit
## 19: stress ratio > sratmax
## species scores not available
## species scores not available
## species scores not available
## species scores not available
## species scores not available
source("Hymenoptera/Com_matrixes_data_exploration_Hymenoptera_3P_Site.R")
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.03$sample_richness_Site0.03, : Ties are present, p-values
## are not corrected.
## Run 0 stress 0.22086
## Run 1 stress 0.2212641
## ... Procrustes: rmse 0.1159116 max resid 0.5053767
## Run 2 stress 0.2508214
## Run 3 stress 0.2215354
## Run 4 stress 0.2703537
## Run 5 stress 0.2316091
## Run 6 stress 0.2202948
## ... New best solution
## ... Procrustes: rmse 0.1129327 max resid 0.481907
## Run 7 stress 0.2225233
## Run 8 stress 0.2240296
## Run 9 stress 0.2515532
## Run 10 stress 0.2374314
## Run 11 stress 0.2290868
## Run 12 stress 0.2220561
## Run 13 stress 0.2245914
## Run 14 stress 0.2194369
## ... New best solution
## ... Procrustes: rmse 0.01442216 max resid 0.04465484
## Run 15 stress 0.2503353
## Run 16 stress 0.2562257
## Run 17 stress 0.2565169
## Run 18 stress 0.2247513
## Run 19 stress 0.2246353
## Run 20 stress 0.2393523
## *** No convergence -- monoMDS stopping criteria:
## 1: no. of iterations >= maxit
## 19: stress ratio > sratmax
## species scores not available
## species scores not available
## species scores not available
## species scores not available
## species scores not available
source("Hymenoptera/Com_matrixes_data_exploration_Hymenoptera_5P_Site.R")
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.05$sample_richness_Site0.05, : Ties are present, p-values
## are not corrected.
## Run 0 stress 0.2315232
## Run 1 stress 0.2499491
## Run 2 stress 0.2290739
## ... New best solution
## ... Procrustes: rmse 0.1131764 max resid 0.4347482
## Run 3 stress 0.2335993
## Run 4 stress 0.2420133
## Run 5 stress 0.2500365
## Run 6 stress 0.2583728
## Run 7 stress 0.2560814
## Run 8 stress 0.240423
## Run 9 stress 0.2196152
## ... New best solution
## ... Procrustes: rmse 0.07547701 max resid 0.3049032
## Run 10 stress 0.2536737
## Run 11 stress 0.2186078
## ... New best solution
## ... Procrustes: rmse 0.05526248 max resid 0.2483082
## Run 12 stress 0.2375132
## Run 13 stress 0.2197507
## Run 14 stress 0.2406202
## Run 15 stress 0.2187457
## ... Procrustes: rmse 0.01125625 max resid 0.04777274
## Run 16 stress 0.2201127
## Run 17 stress 0.2316705
## Run 18 stress 0.2228166
## Run 19 stress 0.2197297
## Run 20 stress 0.2396929
## *** No convergence -- monoMDS stopping criteria:
## 20: stress ratio > sratmax
## species scores not available
## species scores not available
## species scores not available
## species scores not available
## species scores not available
#**We get the diversity analysis at haplotypes, 3% and 5% lineages in Coleoptera**
##Source to scripts Coleoptera and data
source("Coleoptera/Com_matrixes_data_exploration_Coleoptera_h_Site.R")
## Warning in Ops.factor(left, right): '>' not meaningful for factors
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site_h$sample_richness_Site_h, : Ties are present, p-values are
## not corrected.
## Run 0 stress 9.552724e-05
## Run 1 stress 9.692118e-05
## ... Procrustes: rmse 0.0001430887 max resid 0.0003406894
## ... Similar to previous best
## Run 2 stress 9.434765e-05
## ... New best solution
## ... Procrustes: rmse 0.0001218041 max resid 0.0004176262
## ... Similar to previous best
## Run 3 stress 9.907821e-05
## ... Procrustes: rmse 0.0001491776 max resid 0.0005699299
## ... Similar to previous best
## Run 4 stress 9.49929e-05
## ... Procrustes: rmse 0.0002059656 max resid 0.000637209
## ... Similar to previous best
## Run 5 stress 9.588271e-05
## ... Procrustes: rmse 0.0001982477 max resid 0.0004757986
## ... Similar to previous best
## Run 6 stress 9.023621e-05
## ... New best solution
## ... Procrustes: rmse 0.0001112822 max resid 0.0002118612
## ... Similar to previous best
## Run 7 stress 9.346549e-05
## ... Procrustes: rmse 0.0001666722 max resid 0.0005003735
## ... Similar to previous best
## Run 8 stress 9.49311e-05
## ... Procrustes: rmse 0.0001174962 max resid 0.0002521223
## ... Similar to previous best
## Run 9 stress 8.068841e-05
## ... New best solution
## ... Procrustes: rmse 0.000167037 max resid 0.0004579998
## ... Similar to previous best
## Run 10 stress 9.754579e-05
## ... Procrustes: rmse 0.000208667 max resid 0.0005624697
## ... Similar to previous best
## Run 11 stress 9.432962e-05
## ... Procrustes: rmse 0.0001325474 max resid 0.0006154589
## ... Similar to previous best
## Run 12 stress 9.613648e-05
## ... Procrustes: rmse 0.0001156214 max resid 0.00033936
## ... Similar to previous best
## Run 13 stress 9.574783e-05
## ... Procrustes: rmse 0.000174489 max resid 0.0005932774
## ... Similar to previous best
## Run 14 stress 9.739414e-05
## ... Procrustes: rmse 9.54317e-05 max resid 0.0002297472
## ... Similar to previous best
## Run 15 stress 9.184774e-05
## ... Procrustes: rmse 7.365552e-05 max resid 0.0002484014
## ... Similar to previous best
## Run 16 stress 8.726268e-05
## ... Procrustes: rmse 0.0001293308 max resid 0.0006225199
## ... Similar to previous best
## Run 17 stress 9.564366e-05
## ... Procrustes: rmse 0.0002126053 max resid 0.0005995389
## ... Similar to previous best
## Run 18 stress 9.70105e-05
## ... Procrustes: rmse 0.0001296802 max resid 0.0005624632
## ... Similar to previous best
## Run 19 stress 9.618529e-05
## ... Procrustes: rmse 4.728994e-05 max resid 0.0001134518
## ... Similar to previous best
## Run 20 stress 9.64537e-05
## ... Procrustes: rmse 0.0001121901 max resid 0.0002655575
## ... Similar to previous best
## *** Solution reached
## Warning in metaMDS(beta.pair$beta.sim): stress is (nearly) zero: you may
## have insufficient data
## species scores not available
## Run 0 stress 0.1016899
## Run 1 stress 0.1160957
## Run 2 stress 0.1166976
## Run 3 stress 0.1108654
## Run 4 stress 0.1077952
## Run 5 stress 0.1186629
## Run 6 stress 0.1112831
## Run 7 stress 0.1128334
## Run 8 stress 0.1087854
## Run 9 stress 0.1046179
## Run 10 stress 0.108274
## Run 11 stress 0.1104088
## Run 12 stress 0.1030868
## Run 13 stress 0.1086193
## Run 14 stress 0.1087196
## Run 15 stress 0.1030807
## Run 16 stress 0.1072223
## Run 17 stress 0.1111447
## Run 18 stress 0.108601
## Run 19 stress 0.1073821
## Run 20 stress 0.1158125
## *** No convergence -- monoMDS stopping criteria:
## 2: no. of iterations >= maxit
## 18: stress ratio > sratmax
## species scores not available
## species scores not available
## species scores not available
## species scores not available
source("Coleoptera/Com_matrixes_data_exploration_Coleoptera_3P_Site.R")
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.03$sample_richness_Site0.03, : Ties are present, p-values
## are not corrected.
## Run 0 stress 0.1296922
## Run 1 stress 0.1270601
## ... New best solution
## ... Procrustes: rmse 0.09587376 max resid 0.3105905
## Run 2 stress 0.1320351
## Run 3 stress 0.1287044
## Run 4 stress 0.1346142
## Run 5 stress 0.1237186
## ... New best solution
## ... Procrustes: rmse 0.05551642 max resid 0.1596561
## Run 6 stress 0.1363569
## Run 7 stress 0.1366099
## Run 8 stress 0.1410253
## Run 9 stress 0.135464
## Run 10 stress 0.1441057
## Run 11 stress 0.126692
## Run 12 stress 0.1242386
## Run 13 stress 0.1306403
## Run 14 stress 0.1355797
## Run 15 stress 0.1311064
## Run 16 stress 0.1373353
## Run 17 stress 0.1257149
## Run 18 stress 0.1354932
## Run 19 stress 0.1375001
## Run 20 stress 0.1375196
## *** No convergence -- monoMDS stopping criteria:
## 7: no. of iterations >= maxit
## 13: stress ratio > sratmax
## species scores not available
## species scores not available
## Run 0 stress 0.1398926
## Run 1 stress 0.1446353
## Run 2 stress 0.144848
## Run 3 stress 0.1452591
## Run 4 stress 0.1426066
## Run 5 stress 0.1469758
## Run 6 stress 0.1336171
## ... New best solution
## ... Procrustes: rmse 0.08465303 max resid 0.3204013
## Run 7 stress 0.1468523
## Run 8 stress 0.1422256
## Run 9 stress 0.1416075
## Run 10 stress 0.1328955
## ... New best solution
## ... Procrustes: rmse 0.02123241 max resid 0.0541119
## Run 11 stress 0.1471635
## Run 12 stress 0.1484118
## Run 13 stress 0.1441016
## Run 14 stress 0.1470549
## Run 15 stress 0.1499594
## Run 16 stress 0.1498131
## Run 17 stress 0.1472921
## Run 18 stress 0.1472759
## Run 19 stress 0.1471485
## Run 20 stress 0.1345768
## *** No convergence -- monoMDS stopping criteria:
## 20: stress ratio > sratmax
## species scores not available
## species scores not available
## species scores not available
## species scores not available
source("Coleoptera/Com_matrixes_data_exploration_Coleoptera_5P_Site.R")
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.05$sample_richness_Site0.05, : Ties are present, p-values
## are not corrected.
## Run 0 stress 0.1400952
## Run 1 stress 0.1413643
## Run 2 stress 0.1436179
## Run 3 stress 0.1440866
## Run 4 stress 0.1434918
## Run 5 stress 0.1407486
## Run 6 stress 0.1453467
## Run 7 stress 0.1406028
## Run 8 stress 0.1407293
## Run 9 stress 0.1431137
## Run 10 stress 0.1449251
## Run 11 stress 0.1430277
## Run 12 stress 0.1461916
## Run 13 stress 0.1410899
## Run 14 stress 0.1422352
## Run 15 stress 0.1389715
## ... New best solution
## ... Procrustes: rmse 0.07856614 max resid 0.2975092
## Run 16 stress 0.141578
## Run 17 stress 0.1420728
## Run 18 stress 0.1438968
## Run 19 stress 0.1399224
## Run 20 stress 0.1418942
## *** No convergence -- monoMDS stopping criteria:
## 7: no. of iterations >= maxit
## 13: stress ratio > sratmax
## species scores not available
## species scores not available
## Run 0 stress 0.1639448
## Run 1 stress 0.1744695
## Run 2 stress 0.1765964
## Run 3 stress 0.1662604
## Run 4 stress 0.1655517
## Run 5 stress 0.1739224
## Run 6 stress 0.1703355
## Run 7 stress 0.165239
## Run 8 stress 0.1753459
## Run 9 stress 0.1672981
## Run 10 stress 0.1768088
## Run 11 stress 0.1756904
## Run 12 stress 0.1685106
## Run 13 stress 0.1673672
## Run 14 stress 0.1673677
## Run 15 stress 0.166511
## Run 16 stress 0.1638376
## ... New best solution
## ... Procrustes: rmse 0.05350718 max resid 0.2002146
## Run 17 stress 0.16962
## Run 18 stress 0.1713401
## Run 19 stress 0.1647595
## Run 20 stress 0.1641853
## ... Procrustes: rmse 0.0559174 max resid 0.2217796
## *** No convergence -- monoMDS stopping criteria:
## 20: stress ratio > sratmax
## species scores not available
## species scores not available
## species scores not available
## species scores not available
#**We get the diversity analysis at haplotypes, 3% and 5% lineages in Myriapoda**
##Source to scripts Myriapoda and data
source("Myriapoda/Com_matrixes_data_exploration_Myriapoda_h_Site.R")
## Warning in Ops.factor(left, right): '>' not meaningful for factors
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site_h$sample_richness_Site_h, : Ties are present, p-values are
## not corrected.
## Run 0 stress 0.004498111
## Run 1 stress 0.008835104
## Run 2 stress 0.008771117
## Run 3 stress 0.004270409
## ... New best solution
## ... Procrustes: rmse 0.1781292 max resid 0.3303976
## Run 4 stress 0.01515644
## Run 5 stress 0.004248592
## ... New best solution
## ... Procrustes: rmse 0.1320902 max resid 0.3435172
## Run 6 stress 0.003957574
## ... New best solution
## ... Procrustes: rmse 0.107408 max resid 0.2391002
## Run 7 stress 0.02375465
## Run 8 stress 0.007871579
## Run 9 stress 0.003903354
## ... New best solution
## ... Procrustes: rmse 0.1313549 max resid 0.2596707
## Run 10 stress 0.006257089
## Run 11 stress 0.003866141
## ... New best solution
## ... Procrustes: rmse 0.1345201 max resid 0.2196701
## Run 12 stress 0.003861922
## ... New best solution
## ... Procrustes: rmse 0.1441505 max resid 0.3306959
## Run 13 stress 0.0311195
## Run 14 stress 0.006142294
## Run 15 stress 0.00403747
## ... Procrustes: rmse 0.1178921 max resid 0.267503
## Run 16 stress 0.009679839
## Run 17 stress 0.004718485
## Run 18 stress 0.003917166
## ... Procrustes: rmse 0.1523682 max resid 0.3586479
## Run 19 stress 0.004349284
## ... Procrustes: rmse 0.1476007 max resid 0.3107432
## Run 20 stress 0.02559551
## *** No convergence -- monoMDS stopping criteria:
## 20: no. of iterations >= maxit
## species scores not available
## species scores not available
## species scores not available
## species scores not available
source("Myriapoda/Com_matrixes_data_exploration_Myriapoda_3P_Site.R")
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.03$sample_richness_Site0.03, : Ties are present, p-values
## are not corrected.
## Run 0 stress 0.03791431
## Run 1 stress 0.03565255
## ... New best solution
## ... Procrustes: rmse 0.1858931 max resid 0.4179719
## Run 2 stress 0.007639864
## ... New best solution
## ... Procrustes: rmse 0.1651932 max resid 0.3139572
## Run 3 stress 0.04387121
## Run 4 stress 0.03802811
## Run 5 stress 0.03461826
## Run 6 stress 0.04120583
## Run 7 stress 0.03938402
## Run 8 stress 0.03651993
## Run 9 stress 0.03931647
## Run 10 stress 0.007655915
## ... Procrustes: rmse 0.007121302 max resid 0.02997574
## Run 11 stress 0.04842156
## Run 12 stress 0.05042658
## Run 13 stress 0.04225531
## Run 14 stress 0.04611576
## Run 15 stress 0.07827083
## Run 16 stress 0.03277704
## Run 17 stress 0.006114432
## ... New best solution
## ... Procrustes: rmse 0.122026 max resid 0.2434565
## Run 18 stress 0.05375811
## Run 19 stress 0.03870693
## Run 20 stress 0.04523618
## *** No convergence -- monoMDS stopping criteria:
## 10: no. of iterations >= maxit
## 10: stress ratio > sratmax
## species scores not available
## species scores not available
## species scores not available
## species scores not available
source("Myriapoda/Com_matrixes_data_exploration_Myriapoda_5P_Site.R")
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.05$sample_richness_Site0.05, : Ties are present, p-values
## are not corrected.
## Run 0 stress 0.04673913
## Run 1 stress 0.04586795
## ... New best solution
## ... Procrustes: rmse 0.1039306 max resid 0.1882187
## Run 2 stress 0.02858822
## ... New best solution
## ... Procrustes: rmse 0.07512826 max resid 0.2726096
## Run 3 stress 0.05968563
## Run 4 stress 0.01451371
## ... New best solution
## ... Procrustes: rmse 0.1453555 max resid 0.4224504
## Run 5 stress 0.03385359
## Run 6 stress 0.04316031
## Run 7 stress 0.04511632
## Run 8 stress 0.03180625
## Run 9 stress 0.0517851
## Run 10 stress 0.03461956
## Run 11 stress 0.0317859
## Run 12 stress 0.02636104
## Run 13 stress 0.02639511
## Run 14 stress 0.03425297
## Run 15 stress 0.04441202
## Run 16 stress 0.02906087
## Run 17 stress 0.02859055
## Run 18 stress 0.05359923
## Run 19 stress 0.05079672
## Run 20 stress 0.03171714
## *** No convergence -- monoMDS stopping criteria:
## 9: no. of iterations >= maxit
## 11: stress ratio > sratmax
## species scores not available
## species scores not available
## species scores not available
## species scores not available
#**We get the diversity analysis at haplotypes, 3% and 5% lineages in Lepidoptera#**
##Source to scripts Lepidoptera and data
source("Lepidoptera/Com_matrixes_data_exploration_Lepidoptera_h_Site.R")
## Warning in Ops.factor(left, right): '>' not meaningful for factors
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site_h$sample_richness_Site_h, : Ties are present, p-values are
## not corrected.
## Run 0 stress 0.02414004
## Run 1 stress 0.05808426
## Run 2 stress 0.03899857
## Run 3 stress 0.04282035
## Run 4 stress 0.03384725
## Run 5 stress 0.03180344
## Run 6 stress 0.04360861
## Run 7 stress 0.01451009
## ... New best solution
## ... Procrustes: rmse 0.08806015 max resid 0.2833596
## Run 8 stress 0.03180352
## Run 9 stress 0.03735259
## Run 10 stress 0.03452066
## Run 11 stress 0.02797805
## Run 12 stress 0.01452828
## ... Procrustes: rmse 0.02985246 max resid 0.1002764
## Run 13 stress 0.02654015
## Run 14 stress 0.04455215
## Run 15 stress 0.04716167
## Run 16 stress 0.04150023
## Run 17 stress 0.04671479
## Run 18 stress 0.04189623
## Run 19 stress 0.0328243
## Run 20 stress 0.0402562
## *** No convergence -- monoMDS stopping criteria:
## 7: no. of iterations >= maxit
## 13: stress ratio > sratmax
## species scores not available
## species scores not available
## species scores not available
## species scores not available
source("Lepidoptera/Com_matrixes_data_exploration_Lepidoptera_3P_Site.R")
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.03$sample_richness_Site0.03, : Ties are present, p-values
## are not corrected.
## Run 0 stress 0.04662604
## Run 1 stress 0.03266709
## ... New best solution
## ... Procrustes: rmse 0.1381199 max resid 0.3262813
## Run 2 stress 0.02346673
## ... New best solution
## ... Procrustes: rmse 0.1075067 max resid 0.3605672
## Run 3 stress 0.06741553
## Run 4 stress 0.04948565
## Run 5 stress 0.04683001
## Run 6 stress 0.02889005
## Run 7 stress 0.02231042
## ... New best solution
## ... Procrustes: rmse 0.02986127 max resid 0.09613244
## Run 8 stress 0.05941444
## Run 9 stress 0.02570473
## Run 10 stress 0.07045963
## Run 11 stress 0.05115528
## Run 12 stress 0.04600965
## Run 13 stress 0.04079477
## Run 14 stress 0.05300968
## Run 15 stress 0.0445956
## Run 16 stress 0.06981066
## Run 17 stress 0.06068249
## Run 18 stress 0.0433183
## Run 19 stress 0.02350505
## Run 20 stress 0.04116047
## *** No convergence -- monoMDS stopping criteria:
## 5: no. of iterations >= maxit
## 15: stress ratio > sratmax
## species scores not available
## species scores not available
## species scores not available
## species scores not available
source("Lepidoptera/Com_matrixes_data_exploration_Lepidoptera_5P_Site.R")
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.05$sample_richness_Site0.05, : Ties are present, p-values
## are not corrected.
## Run 0 stress 0.09792603
## Run 1 stress 0.08013479
## ... New best solution
## ... Procrustes: rmse 0.1644326 max resid 0.3493958
## Run 2 stress 0.05893182
## ... New best solution
## ... Procrustes: rmse 0.1147131 max resid 0.1946275
## Run 3 stress 0.07636956
## Run 4 stress 0.0742606
## Run 5 stress 0.07259878
## Run 6 stress 0.07394452
## Run 7 stress 0.07260071
## Run 8 stress 0.06958962
## Run 9 stress 0.05867092
## ... New best solution
## ... Procrustes: rmse 0.03790794 max resid 0.1350291
## Run 10 stress 0.08184592
## Run 11 stress 0.04840044
## ... New best solution
## ... Procrustes: rmse 0.0936647 max resid 0.339367
## Run 12 stress 0.04830709
## ... New best solution
## ... Procrustes: rmse 0.04862542 max resid 0.179496
## Run 13 stress 0.07186128
## Run 14 stress 0.04830893
## ... Procrustes: rmse 0.00439486 max resid 0.01804767
## Run 15 stress 0.07431069
## Run 16 stress 0.06673292
## Run 17 stress 0.06931957
## Run 18 stress 0.08147289
## Run 19 stress 0.06931753
## Run 20 stress 0.0713187
## *** No convergence -- monoMDS stopping criteria:
## 20: stress ratio > sratmax
## species scores not available
## species scores not available
## species scores not available
## species scores not available
#**END**